The details modal

Caution

This page is still being edited.

The details modal or details window is opened by clicking on the desired element from element lists. It shows the information stored or available through databases about the element. The modal/window can be set to full screen mode. Its frame is identified by two colors: a dark blue and a light blue. The color light blue means that changes have been made within the modal, but they have not been saved yet. If this is the case, a small save symbol also appears in the modal bar . As soon as you have saved all the entered data, the frame color changes to dark blue and the symbol disappears.

Frame

Tabs were introduced to organize the information within the details modals. They enable information structuring and displaying as in folders. Different tabs are available based on the type of the element. This will become clear in the later chapters.

Details modal for samples#

Details modal Once you have entered and saved the structure of the sample, either with Ketcher or using the Chemical identifiers from the Properties tab, some additional information will be provided automatically. This applies to all information that can be generated by Open Babel based on the structure of your sample (chemical formula, molecular weight). Likewise, the name of your molecule and its exact mass are created automatically, as far as the molecule is known via the PubChem database and this information is available, along with symbols of chemical safety. More details about chemical safety is provided as a link to PubChem too.

Properties tab#

Sample properties The first tab that allows the description of samples is the Properties tab. In the Molecule field, the user can pick the preferred naming convention for their molecule or write a new one. They could also specify the absolute and the relative configuration of the molecule in the fields Stereo Abs, Stereo Rel respectively from drop-downs. The user can mark their confidential data as Top secret.

If you want to assign a name (e.g. a trivial name) to a sample, you can do this by making an entry in the Name or Description fields. Please note that the Name field for samples from reactions is overwritten by additional information. Your created sample will have the selected name, but when a new sample is created by dragging and dropping it into a reaction scheme, the Name field will be overwritten. If you want to save a second or more names for your sample permanently, use the Description field.

Caution

The Name field within the Sample Properties tab is overwritten for samples that represent products in a reaction, because the product Name is required.

In addition to the naming options, an external label can be saved for each sample. This external label should be used to enable your sample to be assigned to another storage system. For example, if you make a sample available for a reference database or send it to a cooperation partner who renames your sample, your sample will receive a sequential number that is not determined by you. Enter this number in the External label field. For participants in the Compound Platform, the External label field is reserved for the X-Vial numbers of the samples.

Solvent can be specified from a predefined drop-down. The Amount can be provided either as mass or in mols, where providing one of them leads to automatic calculation of the other based on the Purity (1 by default but can be modified). Mass unit can be either g or mg, while amount unit is either mol or mmol. Volume data can’t be edited until Density or Molarity are specified, then the volume is automatically calculated. Changing the volume manually leads to automatic changes in the mass and amount.

Both Boiling point and Melting point can be provided manually in Celsius °C. The user can additionally provide any desired information as free text in the Description field and specify the location of the samples (e.g. institute, warehouse, etc.) in the Location field.

The Elemental composition is automatically calculated based on the formula, but the user can still provide their experimental numbers in fields that correspond to each atom in the molecule.

The information required for chemical use is supplemented by Chemical identifiers such as InChI , Canonical SMILLES and CAS number. Molecular structure is also provided in the Molfile format. You can provide the Canonical SMILLES to create a new Sample, but you can’t modify the SMILES after creation. The other identifiers can only be copied after a Sample is created, and they can’t be used to generate Samples.

Analyses tab#

Analyses

To add analytics information to the ELN, the Analyses tab is available. Here the evaluation of the performed analytical experiments can be entered (field Content) and additional files can be uploaded to store the data and its documents (see datasets).

You can create as many analyses for a sample as you need with the button , and for each analysis you can upload as many datasets (files) as you want with the button . Please pay attention to the structure of the data storage and take care of the input fields, this will allow you to search your results quickly. Any information that you define through the created fields is available to the ELN for processing and this data can be displayed or summarized in lists.

The uploaded records can be supplemented with information in an input modal available for each data file. The input modal opens either when you create a new data record, or when you click on the link generated by the name of existing data records.

Analyses that you have entered are shown in short form e.g. in the sample list, and you can find out at a glance which data you have entered. The illustration shows the sample list with symbols such as or . The first case means that you have set an analysis for the analyzed sample, but its Status is so far Unconfirmed. The second symbol informs you again about an existing analysis whose Status has already been Confirmed, and therefore, it is classified by you as correct. The number given always refers to the number of analyses, not to the number of uploaded data files.

The analysis methods, from which you can choose, are given by the drop-down menu Type (Chemical Methods Ontology). You can delete your datasets from within your analysis by clicking , or install it as a zip file with . You shouldn't forget one important property of the ELN: the uploaded data files and entered information are not saved until you confirm that with or . This point if overlooked can lead to the loss of the data you have set.

Literature tab#

Literature

The Literature tab allows you to manage your literature and link it to your Sample. You can specify as many references as you find needed. It is possible to specify the reference either by its DOI or ISBN, or by giving it a title and a URL. In both cases, you can add whether this reference is citing you or cited by you. When all details of a reference are entered, press . Once a reference is created, it cannot be edited, it can only be deleted, so if you need to edit a reference, delete it and create a new one.

The created references are added to a list and they are shown in blue to indicate their functionality in linking to some resources by clicking on them. Each reference can by copied using , which will copy the information provided in the list. Additional details about the reference, as by whom it was created and whether it is referring to or cited by you, can be shown by pressing the button , which also shows the delete button . Don’t forget to save your changes with .

SciFinder tab#

Not available at the moment.

Results tab#

This tab is not supported at the moment as it is still being developed.

QC & curation tab#

Details modal for reactions#

Scheme tab#

The Scheme tab initially contains the scheme of the selected reaction. While the molecular structure of samples (in samples details modal) can be edited by selecting the structure field and opening the Ketcher editor, the reaction Scheme cannot be changed. If the user wants to change their reaction, they have to select the contained samples and change their structure or select other samples.

info

Changing a reaction is not possible by changing its scheme, rather it must be carried out indirectly by selecting or changing the samples.

The following figure shows a typical reaction Scheme with a reagent table. No solvents nor reaction temperature have been added yet. In general, you cannot edit gray fields in the reaction table.
Reagents_table The used samples are classified into Starting materials, Reactants and Products. The samples can be moved flexibly from one category to another with drag & drop symbol . This grouping causes functional differences: The difference between the Starting materials and theReactants lies in the way their corresponding samples are treated upon generation. This will become clear later on in this chapter when discussing adding samples to a reaction. Regarding the Products, their fields can only be modified to a limited extent to avoid misuse of the journal. Certain fields that can be obtained from the received quantity of the product are not open for input. The Products have a special treatment within the reaction, for example the analyses of the corresponding samples are stored and can be found in the Analyses tab.

A reaction can be populated with samples in two different ways:

  1. Create new sample: Reaction create smaples

The user can create new samples by pressing in the corresponding category Starting materials, Reactants or Products. In this case, the Starting materials and the Products samples will be added to the samples list. The Reactants will be saved as samples, and they are initially displayed in the samples list, but when you save the reaction and reload the page, all Reactants are not displayed in the list anymore in order to avoid unnecessary accumulation of samples, which are very often used as reactants. The Reactants samples are still accessible from within the reaction Scheme by pressing the reactant name. The Reactants can be selected from the drop-down menu Reagents, and they are also not added to the samples list.

Recommendation

If you want to see a reactant displayed in the samples list, change its status from Reactants to Starting materials. By definition, Reactants are not displayed in the samples list.

  1. Select samples from the samples list: Reaction drag smaples

The user can select samples from the samples list if they are already there and drag and drop them using either one of the symbols next to its molecular structure or next to the sample name and place the sample in the reaction. If you only want to adopt the molecular structure, then the symbol next to the molecular structure in the sample list must be used for the drag & drop action. The internal process here corresponds to the **copy** action. If you want to carry out a reaction that uses existing samples, e.g. carry out a subsequent reaction and use a product from a previous reaction as starting material or use a chemical from a chemical container, then you should use the symbol next to a sample name in the sample list and place the sample in the reaction using drag & drop. A split of the sample is generated internally in the system (recognizable by the generation of the sample number). This applies only to the Starting materials as dragging and dropping of samples to the Reactants section doesn‘t add anything to the samples list. Splitting is not possible for products, as they always have to be recreated, but copy is possible.

The user can choose either the Starting materials or the Reactants as a reference using the Ref switch. As a result, the selected reference is automatically assigned an equivalent Equiv of 1.000. Several Starting materials and Reactants can be added, but only one sample can be marked as reference material.

Mass can be represented in g, mg or μg, the volume in l, ml, μl, and the amount in mol or mmol. Entering one type of data leads to automatic calculation of the others. The volume is calculated only if the molarity of the sample is already set, and the equivalents are calculated unless the sample is a reference, then it gets a fixed equivalent of 1.000. By entering the mass, volume or amount of the reference, the remaining information for the further samples is calculated as soon as at least either the amount or the Equiv is given for them.

info

When entering the amount of your sample, you can decide which unit you want to use by pressing the unit button next to the number.

Caution

The calculation and display of the volume can only be correct if the molarity of the sample has been entered correctly and precisely in the sample.

An additional function is included within the reaction table, which allows you to differentiate between reaction planning and implementation. You can find the function under the title T/R. means that you can enter/ calculate inputs according to the reaction planning. If you switch from to , you can enter the quantities actually received. This function was created so that in the event of a deviation (e.g. due to accuracy in the dosage) from the planned experiments, the values of both procedures are still available.

Reaction solvents The solvents can be introduced by expanding the gray area Solvents. The user can either pick a solvent from the drop-down Default solvents, or they can use a sample as a solvent, and in this case the sample will be treated the same way as a reactant sample, i.e. it can be created with , but it will not be displayed in the samples list, or if the sample is already in the samples list, it can be dragged and dropped with , but no copy or split will occur here.

The solvent can be given a Label which is transferred to the reaction arrow when updated by the symbol . When specifying the solvents volumes **Vol** (in l, ml, or μl), the molarity of the solution **Conc** is automatically calculated based on the individual samples in the reaction table. You can add as many solvents as you want. If you are using more than one solvent, the volume ratio **Vol ratio** of the solvents to each other is displayed. You can also distinguish between solvent details in the planned and implemented reaction with (planned) and (implemented). Samples and solvents in a reaction can be removed from the reaction using the button .

In the gray area Conditions, the user can Select special conditions required for the reaction from a drop-down menu. Those conditions include UV, microwave, ultrasound, visible light. The selected conditions are added to a field where the user can additionally add other conditions as free text.

Out of the Conditions area, the user can give their reaction a Name and describe it with a Status from a drop-down. The Status is reflected in the list of reactions by a symbol, so you can see at a glance your evaluation of the reactions. The following table shows all the possible Status and the corresponding symbols.

| symbol | Status|

|--------|--------|

| | Planned |

| | Running |

| | Done |

| | Analyses Pending |

| | Successful |

| | Not Successful |

The temperature of a reaction is inserted via the Temperature field. If a Temperature has been defined, it is also displayed on the reaction arrow. When entering the temperature, you can choose between the Kelvin K, Celsius °C and Fahrenheit °F scale. Enter the temperature in the given scale and switch to the desired unit. You can also enter a complex temperature profile by selecting the graph symbol for the temperature field . A window opens that allows you to enter temperature changes with time, and it displays those changes in a chart. Use + to add a temperature change and – to remove it.

The user can specify the Duration of the reaction by adding its Start time and Stop time with the following format: DD/MM/YYYY hh:mm:ss or DD.MM.YYYY hh:mm:ss, then the Duration is automatically calculated. The user can also input current time with the button. The calculated **Duration** can be copied with , or rounded to the next field either in Week(s), Day(s), Hour(s), Minute(s), or Second(s).

you can also choose the Type of your reactions from the Name Reaction Ontology drop-down. And you can assign a Role to the reaction, such as a General Procedure, Parts of GB, and Single. The Description field is intended for recording your reaction implementation. Please give a detailed description of how you carried out the reaction. The Description field is mirrored within the second Properties tab (and vice versa) to give the user the freedom in which tab they would like to maintain the description of the reaction. The same applies to the Name, Status Temperature, and Type fields.

For a quick overview of the Purification methods that you have used to isolate your target compound, a drop-down menu Purification has been introduced. The methods Flash-Chromatography, TLC, HPLC, Extraction, Distillation, Sublimation and Crystallization are available. The selected methods are lined up as a list. Purification Solvents can be added, and they are treated exactly the same way as the reaction Solvents. Description of the purification process can be included in the field Additional information for publication and purification details.

Finally, the user can the reaction, without saving, or as an xlsx file. This applies to all the other tabs.

Properties tab#

Reaction properties

The Properties tab allows you to enter further details on the reaction. In addition to the fields Name, Status, Temperature, and Type (Chemical Methods Ontology) that are already mirrored in Scheme tab, new fields are introduced such as Dangerous Products where you can list whether dangerous substances occur in your reaction and classify their hazard from a drop-down menu.

In order to be able to reproduce the control of a reaction via thin-layer chromatography, two fields have been developed which are supposed to store the solvents used and their ratio on one hand, and the Rf value of the target product of the reaction on the other hand. Please enter the solvent information in the Solvents (parts) field and enter a space then the ratio of solvents to each other according to this example: ethyl acetate/hexane 2:1. You can also provide further details about your thin layer chromatography in the Description field, e.g. the shape of the spots, or special features of the implementation. Here you can also state how the compounds were identified, i.e. which staining solutions were used or which wavelength was selected for the UV detection.

References tab#

The References tab of a reaction is identical to the Literature tab of a sample. It allows you to manage your literature and link it to your reaction. You can specify as many references as you find needed. It is possible to specify the reference either by its DOI or ISBN, or by giving it a title and a URL. In both cases, you can add whether this reference is citing you or cited by you. When all details of a reference are entered, press . Once a reference is created, it cannot be edited, it can only be deleted, so if you need to edit a reference, delete it and create a new one.

The created references are added to a list and they are shown in blue to indicate their functionality in linking to some resources by clicking on them. Each reference can by copied using , which will copy the information provided in the list. Additional details about the reference, as by whom it was created and whether it is referring to or cited by you, can be shown by pressing the button , which also shows the delete button . Don’t forget to save your changes with .

Analyses tab#

The analyses tab of the reaction view differs from the analysis tab of the sample view in essential ways. While a samples can always have analyses, reaction Analyses can only contain Products samples that are supported by analyses. The Analyses tab of the reactions therefore only shows analyses by means of a link. To edit the data, the link (name of the product sample) to the analysis of the sample must be followed.

Green Chemistry tab#

This tab contains fields for green chemistry metrics to quantify the environmental performance of your reaction. Those fields are Simple E factor (sEF), Complete E factor (cEF), Custom E factor, Atom economy (AE), Custom Atom economy. Those metrics are calculated automatically based on the masses of the samples in your reaction, and the waste produced through it. All the reaction samples are shown again in the Green Chemistry tab, with directly unmodifiable details about their Mass, Volume, Moles, and equivalents Eguiv. To modify those fields you need to go back to the corresponding sample and update the numbers, while you can modify the coefficients field Coeff directly from the Green Chemistry tab. The user can specify whether the Starting Materials and the Reactants are Recyclable, and they can specify whether their Products are Waste with a checkbox. If you are facing any problems with ticking the checkbox, make sure that you are using Chrome, and try to save the reaction and reload the page.

SciFinder tab#

Not available at the moment.

Detail modal for wellplates#

Designer tab#

Wellplate designer Wellplate well

The Designer tab graphically displays the wells and shows how they are filled with samples. Since the representation of the individual samples may not be sufficient for some applications due to the limited space, it can be enlarged by selecting the appropriate well within the designer, which provides insight into selected information on the underlying samples and their sample number, Readout and Imported Readout. It also enables deleting the sample from the wellplate with the button . The Readout field can’t be edited from within the Designer tab, but rather from the List tab, while the Imported Readout can be edited from within the sample’s details modal from the Results tab.

List tab#

Wellplate list

the List tab can be used to organize the samples collected in the wellplate. All inserted samples appear automatically in list form according to their assignment in the Designer (Position). The table of the list also contains the information about molecular structure (Molecule), Name, External label, Sum Formula, Readout and Imported Readout. The Readout field values are displayed again in the Designer tab when selecting individual wells.

Properties tab#

Wellplate properties

Properties tab allows you to enter additional information about a wellplate, such as a Name, its Size, which is fixed as 96 at the moment, and a Description.

Analyses tab#

You can create as many analyses for a sample as you need with the button , and for each analysis you can upload as many datasets (files) as you want with the button . Please pay attention to the structure of the data storage and take care of the input fields, this will allow you to search your results quickly. Any information that you define through the created fields is available to the ELN for processing and this data can be displayed or summarized in lists.

The uploaded records can be supplemented with information in an input modal available for each data file. The input modal opens either when you create a new data record, or when you click on the link generated by the name of existing data records.

The analysis methods, from which you can choose, are given by the drop-down menu Type (Chemical Methods Ontology). You shouldn't forget one important property of the ELN: the uploaded data files and entered information are not saved until you confirm that with or . This point if overlooked can lead to the loss of the data you have set.

You can delete your datasets from within your analysis by clicking , or install it as a zip file with

Detail modal for screens#

In the future, it should also be possible to use the ELN for the documentation of biological experiments. The structure of this biological work should be possible through the element Screen. All descriptions and procedures of biological work for a planned experiment are recorded on a screen while the wellplates define the localization of the substances and materials used. Wellplates can therefore also be assigned to the individual screens in order to make their affiliation clear.

So far, only a rudimentary structure for entering the screens has been programmed. The further development is an important task within the project in the coming months. The most important data of a biological study can be saved by entering free text in the Name, Collaborator, Requirements, Conditions, Result and Description fields. The allocation of the wellplates required for the examination can be done via drag & drop directly under the heading Wellplates. The selected wellplates are added and are directly available through a link.

Detail modal for research plan#

Reseach plan A research plan is a generic element that can be used in a flexible manner to describe a particular processes. The research plan be given a Name, and there are plenty of fields that can be added in the form of text (Add Text Editor), tables(Add Table Editor), images (either a molecular structure with Add Ketcher Editor, or a regular image with Add Image where you can control its Zoom ). You can add other elements such as samples (Add Sample) and reactions (Add Reaction) with drag and drop.