Robocrystallographer: Automated crystal structure text descriptions and analysis

Our ability to describe crystal structure features is of crucial importance when attempting to understand structure-property relationships in the solid state. In this paper, the authors introduce robocrystallographer, an open-source toolkit for analyzing crystal structures. This package combines new and existing open-source analysis tools to provide structural information, including the local coordination and polyhedral type, polyhedral connectivity, octahedral tilt angles, component-dimensionality, and molecule-within-crystal and fuzzy prototype identification. Using this information, robocrystallographer can generate text-based descriptions of crystal structures that resemble descriptions written by human crystallographers. The authors use robocrystallographer to investigate the dimensionalities of all compounds in the Materials Project database and highlight its potential in machine learning studies

PEMBUATAN WEB APLIKASI INVENTARIS LABORATORIUM TEKNIK ELEKTRO UMS DENGAN ACTIVE SERVER PAGES ( ASP ) DAN DATABASE OPEN DATABASE CONNECTIVITY ( ODBC )

Pada saat ini proses input alat di laboratorium masih banyak dilakukan secara manual, terutama dalam pencatatan alat masuk dan keluar, laporan-laporan. Hal ini menyebabkan sering timbulnya kesalahan yang dapat berdampak pada keberadaan stock alat. Oleh karena itu, perlu dibutuhkannya proses komputerisasi untuk mengatasi kelemahan tersebut. Pembuatan aplikasi inventaris dimulai dengan membuat desain dari sistem yang digunakan laboratorium saat ini. Setelah model terbentuk lalu dikonfirmasikan dengan admin, untuk memperoleh kesatuan pandangan untuk menyimpan data. Fitur yang dapat diakses oleh admin yang telah login yaitu form pengeditan data alat, form penambahan data alat, laporan stock alat, laporan peminjaman alat,dan laporan penerimaan alat, laporan master alat laboratorium, kemudian tahap selanjutnya adalah merancang database yang digunakan untuk menyimpan data. Aplikasi inventaris laboratorium teknik elektro UMS dengan menggunakan Macromedia Dreamweaver dengan ASP sebagai bahasa script dan Microsoft Access sebagai penyimpan database akan membantu mengatasi masalah mengenai proses mencari data alat laboratorium, jumlah alat laboratorium yang selanjutnya data-data peminjaman dapat dilihat dalam bentuk laporan. Hasil dari perancangan aplikasi yang dibuat adalah web inventaris yang dapat membantu pengguna untuk melakukan input alat laboratorium 24 jam. Penggunaan aplikasi ini dapat memberikan hasil yang cepat, efisien, serta mengatasi kesulitan mencari dan memanipulasi data alat laboratorium

Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database

Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for predicting chemical properties from molecular structure. In this article, the ongoing work to describe the chemical connectivity of entries contained in the Crystallography Open Database (COD) in SMILES format is reported. This collection of SMILES is publicly available for chemical (substructure) search or for any other purpose on an open-access basis, as is the COD itself. The conventions that have been followed for the representation of compounds that do not fit into the valence bond theory are outlined for the most frequently found cases. The procedure for getting the SMILES out of the CIF files starts with checking whether the atoms in the asymmetric unit are a chemically acceptable image of the compound. When they are not (molecule in a symmetry element, disorder, polymeric species,etc.), the previously published cif_molecule program is used to get such image in many cases. The program package Open Babel is then applied to get SMILES strings from the CIF files (either those directly taken from the COD or those produced by cif_molecule when applicable). The results are then checked and/or fixed by a human editor, in a computer-aided task that at present still consumes a great deal of human time. Even if the procedure still needs to be improved to make it more automatic (and hence faster), it has already yielded more than 160,000 curated chemical structures and the purpose of this article is to announce the existence of this work to the chemical community as well as to spread the use of its results.The authors are grateful to the Junta de Andalucía (Research Group FQM-195) for financial support of the publication costs of this article

Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database

Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for predicting chemical properties from molecular structure. In this article, the ongoing work to describe the chemical connectivity of entries contained in the Crystallography Open Database (COD) in SMILES format is reported. This collection of SMILES is publicly available for chemical (substructure) search or for any other purpose on an open-access basis, as is the COD itself. The conventions that have been followed for the representation of compounds that do not fit into the valence bond theory are outlined for the most frequently found cases. The procedure for getting the SMILES out of the CIF files starts with checking whether the atoms in the asymmetric unit are a chemically acceptable image of the compound. When they are not (molecule in a symmetry element, disorder, polymeric species,etc.), the previously published cif_molecule program is used to get such image in many cases. The program package Open Babel is then applied to get SMILES strings from the CIF files (either those directly taken from the COD or those produced by cif_molecule when applicable). The results are then checked and/or fixed by a human editor, in a computer-aided task that at present still consumes a great deal of human time. Even if the procedure still needs to be improved to make it more automatic (and hence faster), it has already yielded more than 160,000 curated chemical structures and the purpose of this article is to announce the existence of this work to the chemical community as well as to spread the use of its results.The authors are grateful to the Junta de Andalucía (Research Group FQM-195) for financial support of the publication costs of this article

Aplikasi Pengolahan Data Bahan Baku dan Data Keuangan Berbasis Data Base Engine pada PT. Sarana Sumber Tirta Kab. Cirebon

Pada Jurnal ini, Penulis melakukan Penelitian pada masalah Analisis DataBase Engine Sistem yang dilakukan pada saat ini menggunakan dua aplikasi yang berbeda yaitu aplikasi Visual Foxpro dan aplikasi Visual Basic, dari kedua aplikasi tersebut digunakan untuk pengolahan Data keuangan dengan aplikasi Visual Basic sedangkan untuk input Data bahan baku menggunakan Visual Foxpro dari kedua aplikasi tersebut masing – masing belum terkoneksi, sehingga jika data persediaan barang sudah terinput, tambah data, hapus data atau koreksi data di Visual foxpro berkas harus dibawa kebagian keuangan dan harus diinput ulang oleh bagian keuangan dengan menggunakan aplikasi Visual Basic, dari hal tersebut diatas walaupun sudah menggunakan komputerisasi namun masih terdapat kekurangan oleh karena itu penulis menyarankan agar menambah konfigurasi dengan menggunakan sistem engine untuk menggabungkan aplikasi tersebut yaitu dengan menggunakan ODBC ( Open Database Connectivity ) merupakan Application Programming Interface ( API ) dimana Database yang digunakan khusus untuk mengakses Database Relasional.Sehingga Alur kerja dari Sistem yang dikerjakan menjadi jelas, dan hasil dari proses kerja menjadi lebih Effektif dan lebih Akura

Open database connectivity development of the context interchange system

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1997.Includes bibliographical references (p. 81-82).by Andy C.Y. Shun.M.Eng

An improved software process management tool: ReMoTe (recursively estimating multi-threaded observation tool enterprise)

The principal purpose of the project is to enable ReMoTe support for multi-databases. ReMoTe stands for the Recursively Estimating Multi-Threaded Observation Technology Enterprise, which is a web-based computer aided software engineering tool for monitoring software development process. Development of ReMoTe is based on the RMT (Recursive Multi-Threaded) software life cycle developed by Scott Simon, a CSUSB alum, in his master\u27s thesis in 1997. ReMoTe enables the monitoring of projects that use different databases in various locations. Central management can view the progress information of each project using a web browser no matter where the database or project team is located. In this project, three database software were supported, namely MySQL, Oracle, and Microsoft Access, and employed contemporary technologies such as JavaScript, PHP, and Open Database Connectivity (ODBC). Source codes are included

Global landscape of mouse and human cytokine transcriptional regulation

Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through three decades of studies to generate a comprehensive database, CytReg, reporting 843 and 647 interactions between TFs and cytokine genes, in human and mouse respectively. By integrating CytReg with other functional datasets, we determined general principles governing the transcriptional regulation of cytokine genes. In particular, we show a correlation between TF connectivity and immune phenotype and disease, we discuss the balance between tissue-specific and pathogen-activated TFs regulating each cytokine gene, and cooperativity and plasticity in cytokine regulation. We also illustrate the use of our database as a blueprint to predict TF–disease associations and identify potential TF–cytokine regulatory axes in autoimmune diseases. Finally, we discuss research biases in cytokine regulation studies, and use CytReg to predict novel interactions based on co-expression and motif analyses which we further validated experimentally. Overall, this resource provides a framework for the rational design of future cytokine gene regulation studies.National Institutes of Health (NIH) [R00 GM114296 and R35 GM128625 to J.I.F.B., 5T32HL007501-34 to J.A.S.]; National Science Foundation [NSF-REU BIO-1659605 to M.M.]. Funding for open access charge: NIH [R35 GM128625]. (R00 GM114296 - National Institutes of Health (NIH); R35 GM128625 - National Institutes of Health (NIH); 5T32HL007501-34 - National Institutes of Health (NIH); NSF-REU BIO-1659605 - National Science Foundation; R35 GM128625 - NIH)Published versio